Search results for "Metabolic Network"
showing 10 items of 115 documents
Genome Sequence of the Methanotrophic Poly-β-Hydroxybutyrate Producer Methylocystis parvus OBBP
2012
-- PAGS 2 5709-5710
Computational annotation of genes differentially expressed along olive fruit development
2009
Abstract Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) a…
Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms.
2019
Mitochondria have been increasingly recognized as a central regulatory nexus for multiple metabolic pathways, in addition to ATP production via oxidative phosphorylation (OXPHOS). Here we show that inducing mitochondrial DNA (mtDNA) stress in Drosophila using a mitochondrially-targeted Type I restriction endonuclease (mtEcoBI) results in unexpected metabolic reprogramming in adult flies, distinct from effects on OXPHOS. Carbohydrate utilization was repressed, with catabolism shifted towards lipid oxidation, accompanied by elevated serine synthesis. Cleavage and translocation, the two modes of mtEcoBI action, repressed carbohydrate rmetabolism via two different mechanisms. DNA cleavage activ…
Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach
2009
International audience; Denitrification is a microbial respiratory process contributing to the emission of greenhouse gas. The study of denitrifying bacteria, like that of others, is hindered by characteristics that can prevent up to 99% of soil bacteria from being cultivated in vitro. New approaches based on the direct extraction of DNA from the natural environment and PCR amplifications can overcome limitations due to bacterial unculturability, but until now their application to denitrification genes has led only to the recovery of partial sequences for some of these genes.Our goals in this study were to apply a metagenomic approach characterized by cloning of DNA extracted from soil and …
Computer simulations for bioequivalence trials: selection of analyte in BCS drugs with first-pass metabolism and two metabolic pathways.
2010
The objective of this work is to use a computer simulation approach to define the most sensitive analyte for in vivo bioequivalence studies of all types of Biopharmaceutics Classification System (BCS) drugs undergoing first-pass hepatic metabolism with two metabolic pathways. A semi-physiological model was developed in NONMEM VI to simulate bioequivalence trials. Four BCS classes (from Class I to IV) of drugs, with three possible saturation scenarios (non-saturation, saturation and saturation of only the major route of metabolism), two (high or low) dose schemes, and six types of pharmaceutical quality for the drug products were simulated. The number of investigated scenarios was 144 (4 × 3…
Hepatocytes--the choice to investigate drug metabolism and toxicity in man: in vitro variability as a reflection of in vivo.
2007
The pharmaceutical industry is committed to marketing safer drugs with fewer side effects, predictable pharmacokinetic properties and quantifiable drug-drug interactions. Drug metabolism is a major determinant of drug clearance and interindividual pharmacokinetic differences, and an indirect determinant of the clinical efficacy and toxicity of drugs. Progressive advances in the knowledge of metabolic routes and enzymes responsible for drug biotransformation have contributed to understanding the great metabolic variations existing in human beings. Phenotypic as well genotypic differences in the expression of the enzymes involved in drug metabolism are the main causes of this variability. How…
Modelling the metabolic shift of polyphosphate-accumulating organisms
2014
Enhanced biological phosphorus removal (EBPR) is one of the most important methods of phosphorus removal in municipal wastewater treatment plants, having been described by different modelling approaches. In this process, the PAOs (polyphosphate accumulating organisms) and GAOs (glycogen accumulating organisms) compete for volatile fatty acids uptake under anaerobic conditions. Recent studies have revealed that the metabolic pathways used by PAOs in order to obtain the energy and the reducing power needed for polyhydroxyalkanoates synthesis could change depending on the amount of polyphosphate stored in the cells. The model presented in this paper extends beyond previously developed metaboli…
Altered brain levels of arachidonic acid-derived inflammatory eicosanoids in a rodent model of anorexia nervosa
2019
Increasing evidence underline the role of inflammation in the behavioral, emotional and cognitive dysregulations displayed in anorexia nervosa (AN). Among the inflammatory mediators acting at both peripheral and central levels, growing attention receives a class of lipids derived from arachidonic acid (AA), called eicosanoids (eiCs), which exert a complex, multifaceted role in a wide range of neuroinflammatory processes, peripheral inflammation, and generally in immune system function. To date, little is known about their possible involvement in the neurobiological underpinnings of AN. The present study evaluated whether the activity-based model of AN (ABA) may alter AA-metabolic pathways b…
A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid
2017
AbstractBacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism –which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphidCinara cedrithat harbors two co-primary endosymbionts,Buchnera aphidicolaBCc andCa.Serratia …
Structural analyses of a hypothetical minimal metabolism
2007
By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal …